Table 1.
Comparison of key features of OmicsNet 2.0 with other web-based tools for multi-omics integration. Symbols used for feature evaluations with ‘√’ for present, ‘-’ for absent and ‘+’ for a more quantitative assessment (more ‘+’ indicate better support). The URL for each tool is given below the table
| Tools | OmicsNet | PaintOmics | MergeOmics | OmicsAnalyst | Arena3D | NeDRex | MetScape |
|---|---|---|---|---|---|---|---|
| Type | Web | Web | Web | Web | Web | Cytoscape plugin | Cytoscape plugin |
| Input | Lists from 8 omics types, graph files | Abundance tables from 5 omics types | Association data, gene sets, networks | Omics feature abundance tables | Graph files | Gene list, gene expression table | Gene expression and metabolomics tables |
| Network creation | |||||||
| SNP annotation | √ | - | √ | - | - | - | - |
| Peak annotation | √ | - | - | - | - | - | - |
| Taxon annotation | √ | - | - | - | - | - | - |
| Network integration | √ | √ | √ | Correlation | Multi-layer | √ | √ |
| Network visualization | |||||||
| 3D view | +++ | - | - | √ | √ | - | |
| 2D view | √ | √ | √ | √ | - | √ | √ |
| Layered layout | +++ | - | - | √ | √ | Cytoscape | Cytoscape |
| Spherical layout | √ | - | - | - | - | - | - |
| Backbone layout | √ | - | - | √ | - | - | - |
| Concentric layout | √ | - | - | √ | - | Cytoscape | Cytoscape |
| Edge bundling | √ | - | - | √ | - | Cytoscape | Cytoscape |
| Network analysis | |||||||
| Enrichment Analysis | +++ | + | +++ | +++ | - | +++ | +++ |
| Joint enrichment analysis | √ | √ | √ | √ | - | - | - |
| Module detection | +++ | - | √ | √ | - | +++ | - |
| Biomarker prioritization | ++ | - | √ | - | - | +++ | - |
• OmicsNet: https://www.omicsnet.ca
• PaintOmics: http://www.paintomics.org
• MergeOmics: http://mergeomics.research.idre.ucla.edu
• OmicsAnalyst: https://www.omicsanalyst.ca
• Arena3Dweb: https://www.arena3d.org
• NedRex: https://nedrex.net
• MetScape: http://metscape.ncibi.org